X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=40f38b6eccbf6e56d063886d9f4203511b5d3826;hb=9ba5a485b66e9c5a86b12dedc7b32616f3ef6db8;hp=84c947710949b8fba80ac52da6f9ce76f98933e1;hpb=f27e64795343e9e4bdf79dab4dacd037e0cb04a6;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 84c9477..40f38b6 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -36,6 +36,7 @@ import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -344,6 +345,8 @@ public abstract class FeatureRendererModel implements
     {
       minmax = new Hashtable<String, float[][]>();
     }
+
+    Set<String> oldGroups = new HashSet<String>(featureGroups.keySet());
     AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -358,9 +361,10 @@ public abstract class FeatureRendererModel implements
       int index = 0;
       while (index < features.length)
       {
+        String fgrp = features[index].getFeatureGroup();
+        oldGroups.remove(fgrp);
         if (!featuresDisplayed.isRegistered(features[index].getType()))
         {
-          String fgrp = features[index].getFeatureGroup();
           if (fgrp != null)
           {
             Boolean groupDisplayed = featureGroups.get(fgrp);
@@ -424,6 +428,16 @@ public abstract class FeatureRendererModel implements
         index++;
       }
     }
+
+    /*
+     * oldGroups now consists of groups that no longer 
+     * have any feature in them - remove these
+     */
+    for (String grp : oldGroups)
+    {
+      featureGroups.remove(grp);
+    }
+
     updateRenderOrder(allfeatures);
     findingFeatures = false;
   }
@@ -561,9 +575,17 @@ public abstract class FeatureRendererModel implements
   public Color getColour(SequenceFeature feature)
   {
     FeatureColourI fc = getFeatureStyle(feature.getType());
-    return fc.getColor(feature);
+    return fc.isColored(feature) ? fc.getColor(feature) : null;
   }
 
+  /**
+   * Answers true unless the feature has a score value which lies outside a
+   * minimum or maximum threshold configured for colouring. This method does not
+   * check feature type or group visibility.
+   * 
+   * @param sequenceFeature
+   * @return
+   */
   protected boolean showFeature(SequenceFeature sequenceFeature)
   {
     FeatureColourI fc = getFeatureStyle(sequenceFeature.type);